Research has continued on developing methodology for analyzing molecular population genetics data. A recently occurring strongly selected substitution is known to reduce neutral genetic variation at linked loci. Using properties of the coalescent process, it is shown that this phenomena continues to hold even if two or more linked strongly selected mutations are simultaneously going to fixation. Work has continued on studying the statistical properties of the sample site frequency spectrum. A statistical test for detecting departures from expectation for a selectively neutral Wright Fisher population was devised and its properties were studied using simulations. The power of the test was also examined for certain alternative models. Since many rare genetic diseases are caused by a single recessive gene that may be maintained in the population, it is of interest to study the effects of a balanced polymorphism on neutral genetic variation at closely linked loci. Extensions of earlier work in this area have been used to investigate the evolutionary consequences of a strongly selected substitution at a locus closely linked to a balanced polymorphism. Preliminary results indicate that the level of neutral variation at a linked locus depends on the locus's position relative to the balanced polymorphism and the strongly selected substitution. Since samples of DNA from diseased persons are not random samples, work has begun on studying the effects of a balanced polymorphism on measures of disequilibrium. These results may be of use in locating a disease gene relative to associated marker genes.